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Assessing environmental changes in Southern Ocean ecosystems is difficult due to its remoteness and data sparsity. Monitoring marine predators that respond rapidly to environmental variation may enable us to track anthropogenic effects on ecosystems. Yet, many long-term datasets of marine predators are incomplete because they are spatially constrained and/or track ecosystems already modified by industrial fishing and whaling in the latter half of the 20th century. Here, we assess the contemporary offshore distribution of a wide-ranging marine predator, the southern right whale (SRW, Eubalaena australis ), that forages on copepods and krill from ~30°S to the Antarctic ice edge (>60°S). We analyzed carbon and nitrogen isotope values of 1,002 skin samples from six genetically distinct SRW populations using a customized assignment approach that accounts for temporal and spatial variation in the Southern Ocean phytoplankton isoscape. Over the past three decades, SRWs increased their use of mid-latitude foraging grounds in the south Atlantic and southwest (SW) Indian oceans in the late austral summer and autumn and slightly increased their use of high-latitude (>60°S) foraging grounds in the SW Pacific, coincident with observed changes in prey distribution and abundance on a circumpolar scale. Comparing foraging assignments with whaling records since the 18th century showed remarkable stability in use of mid-latitude foraging areas. We attribute this consistency across four centuries to the physical stability of ocean fronts and resulting productivity in mid-latitude ecosystems of the Southern Ocean compared with polar regions that may be more influenced by recent climate change.

Restored role of the grey wolf in ecological networks of newly recolonized areas can be studied via surveys of parasite communities of this predator. As helminths circulating in multi-host systems, the tapeworms directly reflect wolves’ diet, while some species are also important from the One Health perspective. The Czech experienced centuries of wolves’ absence, however, now it is situated on the crossroad of recolonising wolves’ populations, which is opening questions of their role in ecological networks in this area and thus in sylvatic cycles of heteroxenous parasites. Five wolf carcasses from this area were obtained and genetic affinity to a particular population was inspected. Tapeworms isolated from wolves’ intestines during necropsies were molecularly identified based on sequences of COI marker. Three wolf haplotypes (w1, w2, w14) correspond with the dominance of haplogroup 1 (w1, w2) within Central European lowland population and haplogroup 2 (w14) within the Carpathian population. Two Taenia spp. were revealed: T. krabbei in Central European population wolves and T. hydatigena in an individual from Carpathian population. The results serve as a base for future monitoring and studies of the recolonising wolf population and its impact on ecosystems in the studied area to contribute to the hypothesis about differentiation of parasite communities in particular wolf population and higher parasite diversity and richness in established populations in comparison to newly settled ones.

Aim: The Expansion-Contraction model has been used to explain the responses of species to climatic changes. During periods of unfavourable climatic conditions, species retreat to refugia from where they may later expand. This paper focuses on the palaeoecology of red deer over the past 54 ka across Europe and the Urals, to reveal patterns of change in their range and explore the role of environmental conditions in determining their distribution. Location: Europe and western Asia to 63°E. Taxon: Red deer (Cervus elaphus). Methods: We collected 984 records of radiocarbon-dated red deer subfossils from the Late Pleistocene and the Holocene, including 93 original dates. For each deer sample we compiled climatic and biome type data for the corresponding time intervals. Results: During the last 54 ka changes in red deer range in Europe and the Urals were asynchronous and differed between western and eastern Europe and western Asia due to different environmental conditions in those regions. The range of suitable areas for deer during the Last Glacial Maximum (LGM) was larger than previously thought and covered vast regions not only in southern but also in western and eastern Europe. Throughout the period investigated the majority of specimens inhabited forests in the temperate climatic zone. The contribution of forests in deer localities significantly decreased during the last 4 ka, due to deforestation of Europe caused by humans. Mean January temperature was the main limiting factor for species distribution. Over 90% of the samples were found in areas where mean January temperature was above −10°C. Main conclusions: Red deer response to climatic oscillations are in agreement with the Expansion-Contraction model but in contradiction to the statement of only the southernmost LGM refugia of the species. During the last 54 ka red deer occurred mostly in forests of the temperate climatic zone. © 2020 John Wiley & Sons Ltd. European Social Fund, Grant/Award Number: UDA-POKL.04.01.01-00-072/09-00; University of Wroclaw, Grant/Award Number: 0410/2990/18; Institute of Environmental Biology, University of Wrocław, Grant/Award Number: 0410/2990/18; Mammal Research Institute Polish Academy of Sciences; Narodowe Centrum Nauki , Grant/Award Number: DEC-2013/11/B/NZ8/00888 and UMO-2016/23/B/HS3/00387; Romanian National Authority for Scientific Research, UEFISCDI, Grant/Award Number: PN-IIIP4-ID-PCE-2016-0676; National Centre for Atmospheric Science and the Centre for Environmental Data Analysis, UK; Faunal Database of the Stage Three Project; Leverhulme Trust, Grant/Award Number: F00568W.

Roosts provide bats with place for daytime sheltering, protection from weather and predators, mating, and social interaction. Movements between multiple roosts are often necessary, either due to limited roost life, changes in roost conditions or demands at different times of the year. Information transfer is an important contributor to day-roosting behaviour and typically exhibits non-random social assortment dynamics. Some individuals appear to explore and share roost discoveries more often than others, though it remains unclear whether associations are stronger between close relatives than less related individuals. In the present study, network analysis, in combination with genetic and spatial data, was used to explore the roosting behaviour of Egyptian fruit bats (Rousettus aegyptiacus) within an isolated deme. Our results showed that the roosts had distinct core-periphery structure. The core of the winter roost network was represented by only two roosts, while in spring, the season of food scarcity, the core was represented by multiple roosts, suggesting their potential role as centres, where information about roosts and foraging sites is exchanged. We found no relationship between relatedness and roost sharing over two seasons. These results provide strong support that Egyptian fruit bats do not roost preferentially with relatives, in contrast to many animal populations where individuals preferentially associate with kin.

The present phylogeographic pattern of red deer in Eurasia is not only a result of the contraction of their distribution range into glacial refugia and postglacial expansion, but probably also an effect of replacement of some red deer s.l. mtDNA lineages by others during the last 50 000 years. To better recognize this process, we analysed 501 sequences of mtDNA cytochrome b, including 194 ancient and 75 contemporary samples newly obtained for this study. The inclusion of 161 radiocarbon-dated samples enabled us to study the phylogeny in a temporal context and conduct divergence-time estimation and molecular dating. Depending on methodology, our estimate of divergence between Cervus elaphus and Cervus canadensis varied considerably (370 000 or 1.37 million years BP, respectively). The divergence times of genetic lineages and haplogroups corresponded to large environmental changes associated with stadials and interstadials of the Late Pleistocene. Due to the climatic oscillations, the distribution of C. elaphus and C. canadensis fluctuated in north–south and east–west directions. Some haplotypes dated to pre-Last Glacial Maximum periods were not detected afterwards, representing possibly extinct populations. We indicated with a high probability the presence of red deer sensu lato in south-eastern Europe and western Asia during the Last Glacial Maximum.

SummaryThe Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s) 1–7. Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM) 8,9, until human persecutions led them to extinction 1–7.There are only seven known Sicilian wolf specimens from the 19th and 20th century preserved in museums in Italy and recent morphometric analyses assigned them to the new subspecies Canis lupus cristaldii10. To better understand the origins of the Sicilian wolf, and its relationship to other wolf populations, we sequenced four whole genomes (3.8×-11.6×) and five mitogenomes. We investigated the relationship between Sicilian wolves and other modern breeds to identify potential admixture. Furthermore, considering that the last land-bridge between Sicily and Italy disappeared after the LGM 11, around 17 kya, we explored the possibility that the Sicilian wolf retained ancestry from ancient wolf and dog lineages. Additionally, we explored whether the long-term isolation might have affected the genomic diversity, inbreeding levels and genetic load of the Sicilian wolf.Our findings show that the Sicilian wolves shared most ancestry with the modern Italian wolf population but are better modelled as admixed with European dog breeds, and shared traces of Eneolithic and Bronze age European dogs. We also find signatures of severe inbreeding and low genomic diversity at population and individual levels due to long-term isolation and drift, suggesting also low effective population size.

X.D. was funded by a grant from the National Institute for Health Research (NIHR) Health Protection Research Unit in Genomics and Enabling Data (no. NIHR200892). M.A.H. was supported by grants from the Medical Research Council (nos. G1001787/1, MR/N002660/1 and MR/P007201/1) and the Economic and Social Research Council (no. ES/S000186/1). E.M.H. was supported by a UK Research and Innovation (UKRI) Fellowship (no. MR/S00291X/1). The discovery of antibiotics more than 80 years ago has led to considerable improvements in human and animal health. Although antibiotic resistance in environmental bacteria is ancient, resistance in human pathogens is thought to be a modern phenomenon that is driven by the clinical use of antibiotics1. Here we show that particular lineages of methicillin-resistant Staphylococcus aureus—a notorious human pathogen—appeared in European hedgehogs in the pre-antibiotic era. Subsequently, these lineages spread within the local hedgehog populations and between hedgehogs and secondary hosts, including livestock and humans. We also demonstrate that the hedgehog dermatophyte Trichophyton erinacei produces two β-lactam antibiotics that provide a natural selective environment in which methicillin-resistant S. aureus isolates have an advantage over susceptible isolates. Together, these results suggest that methicillin resistance emerged in the pre-antibiotic era as a co-evolutionary adaptation of S. aureus to the colonization of dermatophyte-infected hedgehogs. The evolution of clinically relevant antibiotic-resistance genes in wild animals and the connectivity of natural, agricultural and human ecosystems demonstrate that the use of a One Health approach is critical for our understanding and management of antibiotic resistance, which is one of the biggest threats to global health, food security and development. Publisher PDF

Hybridization and introgression have played important roles in the history of various species, including lineage diversification and the evolution of adaptive traits. Hybridization can accelerate the development of reproductive isolation between diverging species, and thus valuable insight into the evolution of reproductive barrier formation may be gained by studying secondary contact zones. Hedgehogs of the genus Erinaceus, which are insectivores sensitive to changes in climate, are a pioneer model in Pleistocene phylogeography. The present study provides the first genome-wide SNP data regarding the Erinaceus hedgehogs species complex, offering a unique comparison of two secondary contact zones between Erinaceus europaeus and E. roumanicus. Results confirmed diversification of the genus during the Pleistocene period, and detected a new refugial lineage of E. roumanicus outside the Mediterranean basin, most likely in the Ponto-Caspian region. In the Central European zone, the level of hybridization was low, whereas in the Russian-Baltic zone, both species hybridise extensively. Asymmetrical gene flow from E. europaeus to E. roumanicus suggests that reproductive isolation varies according to the direction of the crosses in the hybrid zones. However, no loci with significantly different patterns of introgression were detected. Markedly different pre- and post-zygotic barriers, and thus diverse modes of species boundary maintenance in the two contact zones, likely exist. This pattern is probably a consequence of the different age and thus of the different stage of evolution of reproductive isolating mechanisms in each hybrid zone.

AIM: The impact of Pleistocene climatic oscillations on tropical biomes is associated with changes in the extent of forest cover. Fruit bats have played a role in woodland dynamics via pollination and seed dispersal. We hypothesized that phylogeographic patterns of Rousettus on continental Africa and adjacent islands should show a signature of pluvial‐drought cycles, involving demographic expansions and contractions. LOCATION: Afrotropical, Malagasy and Saharo‐Arabian biogeographic realms. TAXON: Genus Rousettus (Pteropodidae). METHODS: Phylogeographic and population genetic approaches using mitochondrial and microsatellite data were integrated with species distribution modelling of currently suitable habitats and those of the Last Glacial Maximum using climate simulations. RESULTS: Phylogenetic reconstruction yielded an Asian outgroup followed by pectinate branching of the Indian Ocean taxa and Rousettus aegyptiacus. While nuclear microsatellites were homogeneous across the African mainland, two mitochondrial haplogroups were found. Haplogroup I is widespread in regions with extensive tree cover, including tropical rain forests, and has close relationships to isolated lineages in the Middle East and islands in the Gulf of Guinea. Haplogroup II is sister to the rest of the R. aegyptiacus radiation and is found in eastern and southern Africa and the Sudanian savanna in habitats with semi‐open land cover. MAIN CONCLUSION: Palaeodistributional modelling ascertained that the Indian Ocean islands provided more extensive areas of suitable habitat in the past relative to conditions today, suggesting stepping stone connectivity between Asia and Africa during Pleistocene interpluvial sea‐level lowstands. Inverse pluvial‐drought demography was detected in lineages ancestral to recent haplogroups, providing evidence of past forest refugia and complex ecogeographic scenarios of haplogroup origins involving allopatry and parapatry connected with the eastern Afromontane biodiversity hotspot, and subsequent admixture of nuclear gene pools. The Middle Eastern lineage probably originated during pluvial green Sahara periods, possibly in co‐evolution with ancestors of tree crop species domesticated later during the Neolithic revolution. The keystone role of rousettine bats for forest regeneration and their ability to pioneer dry and distant habitats emphasize their role in conservation biology and restoration ecology.

Rapid anthropogenic environmental change is expected to impact a host of ecological parameters in Southern Ocean ecosystems. Of critical concern are the consequences of these changes on the range of species that show fidelity to migratory destinations, as philopatry is hypothesized to help or hinder adaptation to climate change depending on the circumstances. Many baleen whales show philopatry to feeding grounds and are also capital breeders that meet migratory and reproductive costs through seasonal energy intake. Southern right whales (Eubalaena australis, SRWs) are capital breeders that have a strong relationship between reproductive output and foraging success. The population dynamics of South Africa's population of SRWs are characterized by two distinct periods: the 1990s, a period of high calving rates; and the late 2010s, a period associated with lowered calving rates. Here we use analyses of stable carbon (δ13C) and nitrogen (δ15N) isotope values from SRW biopsy samples (n = 122) collected during these two distinct periods to investigate foraging ecology of the South African population of SRWs over a time period coincident with the demographic shift. We show that South African SRWs underwent a dramatic northward shift, and diversification, in foraging strategy from 1990s to 2010s. Bayesian mixing model results suggest that during the 1990s, South African SRWs foraged on prey isotopically similar to South Georgia/Islas Georgias del Sur krill. In contrast, in the 2010s, South African SRWs foraged on prey isotopically consistent with the waters of the Subtropical Convergence, Polar Front and Marion Island. We hypothesize that this shift represents a response to changes in preferred habitat or prey, for example, the decrease in abundance and southward range contraction of Antarctic krill. By linking reproductive decline to changing foraging strategies for the first time in SRWs, we show that altering foraging strategies may not be sufficient to adapt to a changing ocean.

The gray wolf Canis lupus range in central Europe is dynamically expanding, reconnecting previously isolated populations. Thus, a recent paper has proposed to merge the current Baltic and Central European (CE) wolf management units, which are no longer isolated by distance. However, recent genetic findings indicate that these two populations are not genetically homogenous. Here we review the most recent data on wolf genetic structure in central Europe and show that even though the CE and Baltic wolves represent the same phylogeographic lineage, their demographic history has resulted in significant genetic structure between these two populations. While the groups are interconnected by moderate gene flow, it is not high enough to reduce the strong founder signal observed in the CE population, suggesting that population dynamics within the CE wolf range are largely independent from those of its source (Baltic) population. Consequently, a management unit combining the CE and Baltic wolves would not form a demographically coherent entity. Thus, we recommend that conservation management units maintain their separate status.

Restored role of the grey wolf in ecological networks of newly recolonized areas can be studied via surveys of parasite communities of this predator. As helminths circulating in multi-host systems, the tapeworms directly reflect wolves' diet, while some species are also important from the One Health perspective. The Czech experienced centuries of wolves' absence, however, now it is situated on the crossroad of recolonising wolves' populations, which is opening questions of their role in ecological networks in this area and thus in sylvatic cycles of heteroxenous parasites.Five wolf carcasses from this area were obtained and genetic affinity to a particular population was inspected. Tapeworms isolated from wolves' intestines during necropsies were molecularly identified based on sequences of COI marker.Three wolf haplotypes (w1, w2, w14) correspond with the dominance of haplogroup 1 (w1, w2) within Central European lowland population and haplogroup 2 (w14) within the Carpathian population. Two Taenia spp. were revealed: T. krabbei in Central European population wolves and T. hydatigena in an individual from Carpathian population.The results serve as a base for future monitoring and studies of the recolonising wolf population and its impact on ecosystems in the studied area to contribute to the hypothesis about differentiation of parasite communities in particular wolf population and higher parasite diversity and richness in established populations in comparison to newly settled ones.

Simple Summary Hedgehogs are regularly brought to wildlife shelters. Depending on the area from where animals are accepted, translocation can occur between different regions or populations. In this study, the genetic diversity of wild hedgehog populations was compared with “shelter populations” within central Europe focusing on the western contact zone between both European hedgehog species. Some shelters were hosting both species at the same time, in one this could be shown genetically. Generally, no difference in genetic diversity between shelter individuals and wild populations was found. Two shelters from Innsbruck hosted individuals that probably belong to two subpopulations. This indicates that shelter management-related translocations could facilitate gene flow across a dispersal barrier. Abstract Hedgehogs are among the most abundant species to be found within wildlife shelters and after successful rehabilitation they are frequently translocated. The effects and potential impact of these translocations on gene flow within wild populations are largely unknown. In this study, different wild hedgehog populations were compared with artificially created “shelter populations”, with regard to their genetic diversity, in order to establish basic data for future inferences on the genetic impact of hedgehog translocations. Observed populations are located within central Europe, including the species Erinaceus europaeus and E. roumanicus. Shelters were mainly hosting one species; in one case, both species were present syntopically. Apart from one exception, the results did not show a higher genetic diversity within shelter populations, indicating that individuals did not originate from a wider geographical area than individuals grouped into one of the wild populations. Two shelters from Innsbruck hosted individuals that belonged to two potential clusters, as indicated in a distance analysis. When such a structure stems from the effects of landscape elements like large rivers, the shelter management-related translocations might lead to homogenization across the dispersal barrier.

Understanding the ecological, behavioural and evolutionary response of organisms to changing environments is of primary importance in a human-altered world. It is crucial to elucidate how human activities alter gene flow and what are the consequences for the genetic structure of a species. We studied two lineages of the Egyptian fruit bat (Rousettus aegyptiacus) throughout the contact zone between mesic and arid Ecozones in the Middle East to evaluate the species' response to the growing proportion of human-altered habitats in the desert. We integrated population genetics, morphometrics and movement ecology to analyse population structure, morphological variation and habitat use from GPS- or radio-tagged individuals from both desert and Mediterranean areas. We classified the spatial distribution and environmental stratification by describing physical–geographical conditions and land cover. We analysed this information to estimate patch occupancy and used an isolation-by-resistance approach to model gene flow patterns. Our results suggest that lineages from desert and Mediterranean habitats, despite their admixture, are isolated by environment and by adaptation supporting their classification as ecotypes. We found a positive effect of human-altered habitats on patch occupancy and habitat use of fruit bats by increasing the availability of roosting and foraging areas. While this commensalism promotes the distribution of fruit bats throughout the Middle East, gene flow between colonies has not been altered by human activities. This discrepancy between habitat use and gene flow patterns may, therefore, be explained by the breeding system of the species and modifications of natal dispersal patterns., This work was funded by the Israel Science Foundation (ISF) Grants ISF‐FIRST 1316/05 and ISF 1259/09, the Grant Agency of the Academy of Sciences of the Czech Republic (IAA 601110905) and the Institutional Research Support grant No. SVV 260 313/2016, the Adelina and Massimo Della Pergolla Chair of Life Sciences and the Minerva Center for Movement Ecology (R.N.), the President of Israel Doctoral Award (D.S.), the Lady Davis Fellowship Trust and the University Pablo de Olavide (A.C‐C).

As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile-Peru (nnew mtDNA/ microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/ microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile-Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile-Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile-Peru. Fil: Carroll, Emma L. University of St. Andrews; Reino Unido Fil: Ott, Paulo H.. Universidade Federal do Rio Grande do Sul; Brasil Fil: McMillan, Louise F.. University Of Wellington; Nueva Zelanda Fil: Vernazzani, Bárbara Galletti. Centro de Conservación Cetacea; Chile Fil: Neveceralova, Petra. Charles University; República Checa Fil: Vermeulen, Els. University Of Pretoria; Sudáfrica Fil: Gaggiotti, Oscar E.. University of St. Andrews; Reino Unido Fil: Andriolo, Artur. Universidade Federal de Juiz de Fora; Brasil Fil: Scott Baker, C.. State University of Oregon; Estados Unidos Fil: Bamford, Connor. British Antarctic Survey; Reino Unido Fil: Best, Peter. University Of Pretoria; Sudáfrica Fil: Cabrera, Elsa. Centro de Conservación Cetacea; Chile Fil: Calderan, Susannah. Scottish Association For Marine Science; Reino Unido Fil: Chirife, Andrea. Universidad Andrés Bello; Chile Fil: Fewster, Rachel M.. University of Auckland; Nueva Zelanda Fil: Flores, Paulo A. C.. No especifíca; Fil: Frasier, Timothy. Saint Marys University; Canadá Fil: Freitas, Thales R.O.. Universidade Federal do Rio Grande do Sul; Brasil Fil: Groch, Karina. Instituto Australis; Brasil Fil: Hulva, Pavel. Charles University; República Checa Fil: Kennedy, Amy. No especifíca; Fil: Leaper, Russell. No especifíca; Fil: Leslie, Matthew S.. No especifíca; Fil: Moore, Michael. No especifíca; Fil: Oliveira, Larissa. Universidade Federal do Rio Grande do Sul; Brasil Fil: Seger, Jon. University of Utah; Estados Unidos Fil: Stepien, Emilie N.. University Aarhus; Dinamarca Fil: Valenzuela, Luciano Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; Argentina Fil: Zerbini, Alexandre. University of Washington; Estados Unidos Fil: Jackson, Jennifer A.. No especifíca

Animals are faced with a range of ecological constraints that shape their behavioural decisions. Habitat features that affect resource abundance will also have an impact, especially as regards spatial distribution, which will in turn affect associations between the animals. Here we utilised a network approach, using spatial and genetic data, to describe patterns in use of space (foraging sites) by free-ranging Egyptian fruit bats (Rousettus aegyptiacus) at the Dakhla Oasis in Egypt. We observed a decrease in home range size during spring, when food availability was lowest, which was reflected by differences in space sharing networks. Our data showed that when food was abundant, space sharing networks were less connected and more related individuals shared more foraging sites. In comparison, when food was scarce the bats had few possibilities to decide where and with whom to forage. Overall, both networks had high mean degree, suggesting communal knowledge of predictable food distribution.

Local extinction and recolonization events can shape genetic structure of subdivided animal populations. The gray wolf (Canis lupus) was extirpated from most of Europe, but recently recolonized big part of its historical range. An exceptionally dynamic expansion of wolf population is observed in the western part of the Great European Plain. Nonetheless, genetic consequences of this process have not yet been fully understood. We aimed to assess genetic diversity of this recently established wolf population in Western Poland (WPL), determine its origin and provide novel data regarding the population genetic structure of the grey wolf in Central Europe. We utilized both spatially explicit and non-explicit Bayesian clustering approaches, as well as a model-independent, multivariate method DAPC, to infer genetic structure in large dataset (881 identified individuals) of wolf microsatellite genotypes. To put the patterns observed in studied population into a broader biogeographic context we also analyzed a mtDNA control region fragment widely used in previous studies. In comparison to a source population, we found slightly reduced allelic richness and heterozygosity in the newly recolonized areas west of the Vistula river. We discovered relatively strong west-east structuring in lowland wolves, probably reflecting founder-flush and allele surfing during range expansion, resulting in clear distinction of WPL, eastern lowland and Carpathian genetic groups. Interestingly, wolves from recently recolonized mountainous areas (Sudetes Mts, SW Poland) clustered together with lowland, but not Carpathian wolf populations. We also identified an area in Central Poland that seems to be a melting pot of western, lowland eastern and Carpathian wolves. We conclude that the process of dynamic recolonization of Central European lowlands lead to the formation of a new, genetically distinct wolf population. Together with the settlement and establishment of packs in mountains by lowland wolves and vice versa, it suggests that demographic dynamics and possibly anthropogenic barriers rather than ecological factors (e.g. natal habitat-biased dispersal patterns) shape the current wolf genetic structure in Central Europe.

Miniopterus schreibersii is a cave-dwelling bat species with a wide distribution in the western Palearctic spanning southern and central Europe, North Africa, Anatolia, the Middle East, and the Caucasus. We investigated the social structure and its effects on the genetic makeup of this species, using 10 nuclear microsatellite markers and a partial fragment of the mitochondrial cytochrome b gene. Samples were examined from the species' entire circum-Mediterranean range. Local structuring that was previously detected among populations of M. schreibersii using mitochondrial markers was not observed for microsatellite markers, indicating male-biased dispersal for the species. Some support was found for postglacial expansions in Europe, with Anatolia potentially acting as the primary refugium during the Last Glacial Maximum (LGM). However, support for this hypothesis is not as strong as that previously detected using mitochondrial DNA markers. This is likely due to the diminishing effect of male-mediated dispersal, replenishing the nuclear diversity faster than the mitochondrial diversity in regions that are relatively far from the glacial refugia.

Cesky Fousek is considered to be one of the oldest pointing dog breeds in Europe and has been appreciated for its versatile working skills. Because it faced extinction in the past, the Cesky Fousek was restored from German Wirehaired and Shorthaired Pointers. Additionally, the breed was recently used in the USA with the initial intent of improvement of the Wirehaired Pointing Griffon (synonymous with Korthals Griffon) by the Bohemian Wirehaired Pointing Griffon Club of America. This study evaluates genetic diversity parameters of Cesky Fousek and compares them to the other continental pointing dogs that played a role in the formation of its gene pool. DNA from buccal swab and blood samples (n = 405) were analyzed using 18 microsatellite markers. Parameters of genetic polymorphism show that the Cesky Fousek breed has a comparable rate of variation as other hunting breeds despite the low population size and severe historical bottlenecks. Clustering analyses reveal a unique genetic status as a distinct pointing dog breed and the relatedness of the breeds is in good concordance with historical data. The present study demonstrates that despite historical admixture among lineages, separate pointing breeds constitute genetically differentiated units, mirroring unique breeding stocks and pedigree isolation among specific breed clubs, reflecting differences in breeding programs under each association.

Cold tolerant species often exhibit specific responses to Pleistocene climate oscillations, including range expansions during glacial periods and altitudinal shifts between glacial and interglacial periods. Small terrestrial mammals are ideal candidates to study these processes due to their limited dispersal abilities, short generation time and rapid sequence evolution. The aim of this study was to investigate phylogeographical structure of the Alpine shrew (Sorex alpinus) within its recently fragmented range in the central and southern European mountain system. To examine its genetic structure, we sequenced the hypervariable domain of the mitochondrial control region in 51 individuals from 18 localities, covering the majority of the distributional area of the species. We analyzed the sequence dataset using population and landscape genetic approaches. We discovered shallow mitochondrial genealogy with degree of differentiation among site-specific haplogroups. This pattern, together with demographic analyses showing population expansion, corroborate the hypothesis that during the glacial periods, S. alpinus expanded its range into lower elevations between northern and high mountain system glaciers. This expansion was followed by a postglacial range breakup, retreat to moderate elevations of high mountain systems, and a formation of relict enclaves in smaller hilly areas.

WOS: 000375896000026, PubMed ID: 27001602, The isolation of populations in the Iberian, Italian and Balkan peninsulas during the ice ages define four main paradigms that explain much of the known distribution of intraspecific genetic diversity in Europe. In this study we investigated the phylogeography of a wide-spread bat species, the bent-winged bat, Miniopterus schreibersii around the Mediterranean basin and in the Caucasus. Environmental Niche Modeling (ENM) analysis was applied to predict both the current distribution of the species and its distribution during the last glacial maximum (LGM). The combination of genetics and ENM results suggest that the populations of M. schreibersii in Europe, the Caucasus and Anatolia went extinct during the LGM, and the refugium for the species was a relatively small area to the east of the Levantine Sea, corresponding to the Mediterranean coasts of present-day Syria, Lebanon, Israel, and northeastern and northwestern Egypt. Subsequently the species first repopulated Anatolia, diversified there, and afterwards expanded into the Caucasus, continental Europe and North Africa after the end of the LGM. The fossil record in Iberia and the ENM results indicate continuous presence of Miniopterus in this peninsula that most probably was related to the Maghrebian lineage during the LGM, which did not persist afterwards. Using our results combined with similar findings in previous studies, we propose a new paradigm explaining the general distribution of genetic diversity in Europe involving the recolonization of the continent, with the main contribution from refugial populations in Anatolia and the Middle East. The study shows how genetics and ENM approaches can complement each other in providing a more detailed picture of intraspecific evolution. (C) 2016 Elsevier Inc. All rights reserved., Research Fund of Bogazici University, Istanbul [08M104, 09S101, 11Y00P2]; Scientific and Technological Research Council of Turkey, TUBITAK [112T698]; Fundacao para a Ciencia e Tecnologia [IF/0497/2013]; IRCSET-Marie Curie International Mobility Fellowship in Science, Engineering and Technology; Ministry of Culture of the Czech Republic [DKRVO 00023272], We would like to thank Elizabeth Hemond and three anonymous reviewers for their comments on an earlier version of the manuscript. We also would like to thank Simos Demetropoulos, Petros Lymperakis, Dina Kovac, Vida Zrncic, Darija Josic, Sanja Drakulic, Tea Knapic, Yannis Kazoglou, Elena Papadatou, Xavier Gremillet, Monika Podgorelec, Peter Vallo, Thierry Disca, Vincent Prie, members of the Win-timdouine expedition (Morocco), Wassim M. Hizem, Pr. Said Nouira, and the "Direction generale des fork de Tunisie" for their assistance with the fieldwork. This study was supported by grants from the Research Fund of Bogazici University, Istanbul (08M104, 09S101 and 11Y00P2) and the Scientific and Technological Research Council of Turkey, TUBITAK (112T698) to RB, from Fundacao para a Ciencia e Tecnologia (research contract IF/0497/2013) to HR, from the IRCSET-Marie Curie International Mobility Fellowship in Science, Engineering and Technology to SJP, and from the Ministry of Culture of the Czech Republic (# DKRVO 00023272) to PB.

Anthropogenic hybridization is widely perceived as a threat to the conservation of biodiversity. Nevertheless, to date, relevant policy and management interventions are unresolved and highly convoluted. While this is due to the inherent complexity of the issue, we hereby hypothesize that a lack of agreement concerning management goals and approaches, within the scientific community, may explain the lack of social awareness on this phenomenon, and the absence of effective pressure on decision-makers. By focusing on wolf x dog hybridization in Europe, we hereby (a) assess the state of the art of issues on wolf x dog hybridization within the scientific community, (b) assess the conceptual bases for different viewpoints, and (c) provide a conceptual framework aiming at reducing the disagreements. We adopted the Delphi technique, involving a three-round iterative survey addressed to a selected sample of experts who published at Web of Science listed journals, in the last 10 years on wolf x dog hybridization and related topics. Consensus was reached that admixed individuals should always be defined according to their genetic profile, and that a reference threshold for admixture (i.e., q-value in assignment tests) should be formally adopted for their identification. To mitigate hybridization, experts agreed on adopting preventive, proactive and, when concerning small and recovering wolf populations, reactive interventions. Overall, experts' consensus waned as the issues addressed became increasingly practical, including the adoption of lethal removal. We suggest three non-mutually exclusive explanations for this trend: (i) value-laden viewpoints increasingly emerge when addressing practical issues, and are particularly diverging between experts with different disciplinary backgrounds (e.g., ecologists, geneticists); (ii) some experts prefer avoiding the risk of potentially giving carte blanche to wolf opponents to (illegally) remove wolves, based on the wolf x dog hybridization issue; (iii) room for subjective interpretation and opinions result from the paucity of data on the effectiveness of different management interventions. These results have management implications and reveal gaps in the knowledge on a wide spectrum of issues related not only to the management of anthropogenic hybridization, but also to the role of ethical values and real-world management concerns in the scientific debate.

Less than 200 wild individuals of the critically endangered Western Derby eland (Taurotragus derbianus derbianus) live in the Niokolo Koba National Park (NKNP) in Senegal. A semi-captive breeding programme was established in 2000 with six founding individuals (one male, five females) transferred from the NKNP. In 2013, the population consisted of 92 individuals living in seven separate herds in the two fenced reserves of Bandia and Fathala in Senegal. Because of the low number of founding individuals in the breeding programme and the resulting high kinship, we compared the results from genealogical and genetic approaches to assess the level of genetic diversity. We used the data from the founder, F1 and F2 generations. In F1, the founder contribution was highly biased towards the only founding male, which sired all the offspring. In F2, the founder contributions were more balanced, as the male descendants of founding females entered the reproduction. This resulted in higher genetic diversity and lower inbreeding (based on pedigree data) in F2 than in F1. Results of molecular analysis using microsatellite loci confirmed the highest level of heterozygosity and lowest level of inbreeding in the founder generation; however, the implementation of a management strategy was not reflected in the empirical results. The results differed for F2, where empirical values of heterozygosity continued to decrease and inbreeding continued to increase. However, the allelic richness corresponded with the results of pedigree analyses, reflecting the more equalized founder contributions. We conclude that the overall results for genetic parameters were comparable with other breeding programmes for endangered ungulates. Nevertheless, we suggest the use of comprehensive molecular data to refine the studbook and to correct relatedness of founders and assign the missing paternities. Our suggestions correspond with the Western Derby Eland Conservation Strategy and confirm the need to introduce new founders into the semi-captive population, in order to minimize the risk of inbreeding depression and improve genetic diversity and suitability for potential reintroduction.

The Mediterranean Basin is typified by a high degree of species rarity and endemicity that reflects its position, geomorphology, and history. Although the composition and cryptic variation of the bat faunas from the Iberian and Balkan Peninsulas are relatively well studied, data from the Apennine Peninsula are still incomplete. This is a significant shortfall, given the presumed refugial role of this region in the context of Europe's Pleistocene phylogeography. It was thus our aim to supplement the phylogeographical information from the region, generating mitochondrial sequences and reviewing published data, with a focus on the dispersal and diversification patterns characterizing taxa with different life strategies. Site-specific lineages were ascertained, especially in the genera Myotis and Plecotus and amongst the pipistrelloid bats, representing speciose radiations. It was possible to observe disjunct ranges with patches isolated south of the Alps in several species, corresponding with evolution of elevated genetic distance. The genetic subdivision within the continuous Italian range into northern and southern lineages in several taxa indicated the possible past substructure of the refugium. Several shared lineages between the Apennine and Ibero-Maghrebian regions were observed, indicating connectivity between the Adriatic and Atlantic−Mediterranean refuges, and raising questions as to which region these clades originated from and what was the direction of faunal exchange between them. In contrast to Europe's other two main refugia, the Apennine Peninsula is a smaller region with simpler phylogeographical patterns. Nevertheless, our results support the idea that the region generated novel lineages. Whereas diversification in sedentary bats may have been driven through the generation of in situ adaptations, specialization, and niche differentiation, the emergence of species with a tramp strategy could have entailed the utilization of faunal drift and the taxon cycle. © 2015 The Linnean Society of London

Retroviruses can create endogenous forms on infiltration into the germline cells of their hosts. These forms are then vertically transmitted and can be considered as genetic fossils of ancient viruses. All retrovirus genera, with the exception of deltaretroviruses, have had their representation identified in the host genome as a virus fossil record. Here we describe an endogenous Deltaretrovirus, identified in the germline of long-fingered bats (Miniopteridae). A single, heavily deleted copy of this retrovirus has been found in the genome of miniopterid species, but not in the genomes of the phylogenetically closest bat families, Vespertilionidae and Cistugonidae. Therefore, the endogenization occurred in a time interval between 20 and 45 million years ago. This discovery closes the last major gap in the retroviral fossil record and provides important insights into the history of deltaretroviruses in mammals.

With the recent and continuing discovery of further cryptic bat species, it is essential to find morphological species discriminating characters. Pipistrellus pipistrellus (common pipistrelle) and Pipistrellus pygmaeus (soprano pipistrelle) have been recognized as separate species since 1997, but no reliable morphological species discriminating trait has yet been found. The most commonly used morphological species discrimination traits are ‘wing vein’ pattern and shape and color of the penis, but these have not been validated on sets of genetically identified specimens. The baculum (os penis) has long been used successfully in species discrimination in bats and other mammals. In this study, we tested the reliability of the established traits and demonstrated how to reliably separate the common pipistrelle and the soprano pipistrelle by simple baculum measurements. The bacula of museum specimens of these two species and of Pipistrellus hanaki were imaged with high-resolution microCT. Several measurements were taken on the size-calibrated volume images, and their value for species discrimination was tested by discriminant analysis with leave-one-out cross validation. We showed that P. pipistrellus and P. pygmaeus specimens can be discriminated by measuring the projected length, height, and width of the baculum (n = 48; all but one classified correctly). Geometric morphometrics was used to analyze and locate variations in baculum shape. Principal component analysis of baculum variation was not sufficient to separate these species. Most of the interspecific variation in baculum shape can be found in the proximal third (the base) of the baculum, and most individual variation can be observed in lateral view, especially in the dorsoventral curve. Quantitative details of morphology are becoming more important to distinguish cryptic species and understand their phylogeographic distributions. The simple baculum measurements can be used to classify single specimens and could be taken without microCT, on a resected baculum.

Conventional monitoring tools are seldom effective for studying the ecology of rare and elusive mammals. In the present study, we use automated ultrasound detectors to provide information about seasonal activity of the greater noctule bat (Nyctalus lasiopterus), the largest and one of least known European bats. We selected localities within Central Europe with diverse geomorphological contexts, including rivers of different sizes and mountain passes. The study demonstrates the capability of the automatic recording approach to achieve bioacoustic discrimination of this species, but also pointed to the persistent need of integrating results from automatic classification software applications with the feedback from manual approaches. The high throughput capacity of the assay proved to be efficient, and the regular occurrence of the species was identified at two localities. These locations are associated with two known and intensely used migratory corridors of winged animals going through Vltava River valley and Cervenohorske Saddle in Jeseniky mountains, as illustrated also by the activity patterns of other migratory species. Together with the occurrence of spring and autumn peaks in activity, these findings are in concordance with the plesiomorphic condition in pipistrelloid bats, showing also migratory behavior, and represent further indirect evidence of migration of the greater noctule. This pattern could be facilitated by the trophic niche of the species, involving predation of migrating songbirds. Differences in phenology of migratory species observed at particular sites likely mirror position of the locality in relation to migration flyways, seasonal and geographic variation in prey availability and energy demands etc. Further application of bioacoustic monitoring and other tools is necessary to obtain detailed information about the range and movement ecology of the species in higher latitudes.

The crucial steps in biological invasions, related to the shaping of genetic architecture and the current evolution of adaptations to a novel environment, usually occur in small populations during the phases of introduction and establishment. However, these processes are difficult to track in nature due to invasion lag, large geographic and temporal scales compared with human observation capabilities, the frequent depletion of genetic variance, admixture and other phenomena. In this study, we compared genetic and historical evidence related to the invasion of the West European hedgehog to New Zealand to infer details about the introduction and establishment. Historical information indicates that the species was initially established on the South Island. A molecular assay of populations from Great Britain and New Zealand using mitochondrial sequences and nuclear microsatellite loci was performed based on a set of analyses including approximate Bayesian computation, a powerful approach for disentangling complex population demographies. According to these analyses, the population of the North Island was most similar to that of the native area and showed greatest reduction in genetic variation caused by founder demography and/or drift. This evidence indicated the location of the establishment phase. The hypothesis was corroborated by data on climate and urbanization. We discuss the contrasting results obtained by the molecular and historical approaches in the light of their different explanatory power and the possible biases influencing the description of particular aspects of invasions, and we advocate the integration of the two types of approaches in invasion biology.

Miniopterus schreibersii is a complex, polytypic species group with a wide distribution ranging from Northern Africa, Southern Europe to Asia, the Solomon Islands and Northern Australia. Two subspecies previously recognized in Turkey, M. s. schreibersii and M. s. pallidus, differ significantly in nuclear and mitochondrial DNA, and in morphology. Until now, the distribution records of M. s. schreibersii and M. s. pallidus showed that they were allopatric and hence even though there was clear morphological and genetic differentiation between the two taxa, whether they represented separate species or subspecies was still not determined with certainty. Here we present the first data on syntopic occurrence of both forms in three caves in south-eastern Turkey. We show that the three caves host individuals of both taxa by using mitochondrial DNA, nuclear DNA and morphometric analyses. These findings provide the final line of evidence to date, for designation of M. s. schreibersii and M. s. pallidus as two separate species, M. schreibersii and M. pallidus. This will raise the number of species in the Eurobats agreement area from 45 to 46.

Here, we present a study of the population genetic architecture and microevolution of the Egyptian fruit bat (Rousettus aegyptiacus) at the environmental margins in the Middle East using mitochondrial sequences and nuclear microsatellites. In contrast to the rather homogenous population structure typical of cave-dwelling bats in climax tropical ecosystems, a relatively pronounced isolation by distance and population diversification was observed. The evolution of this pattern could be ascribed to the complicated demographic history at higher latitudes related to the range margin fragmentation and complex geomorphology of the studied area. Lineages from East Africa and Arabia show divergent positions. Within the northwestern unit, the most marked pattern of the microsatellite data set is connected with insularity, as demonstrated by the separate status of populations from Saharan oases and Cyprus. These demes also exhibit a reduction in genetic variability, which is presumably connected with founder effects, drift and other potential factors related to island evolution as site-specific selection. Genetic clustering indicates a semipermeability of the desert barriers in the Sahara and Arabian Peninsula and a corridor role of the Nile Valley. The results emphasize the role of the island environment in restricting the gene flow in megabats, which is also corroborated by biogeographic patterns within the family, and suggests the possibility of nascent island speciation on Cyprus. Demographic analyses suggest that the colonization of the region was connected to the spread of agricultural plants; therefore, the peripatric processes described above might be because of or strengthened by anthropogenic changes in the environment.